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"Yesterday, there were 6.3 million people in Gotham City. Today...Not so many. The only people left on the streets are the sort that enjoy the chaos. Scum...Criminals...And worse. Not enough good people left to stop them."

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Police Commissioner James W. Gordon dedicated his career to cleaning up the corruption in the Gotham City police department, a goal he has come a long way towards accomplishing. He has been equally tough on crime, and in the pursuit of making Gotham City safe for all its citizens, Gordon has forged an uneasy alliance with Gotham's other top crime fighter, the mysterious vigilante known as Batman.

Gordon with Batman watching as the Arkham Asylum Guards escort the Joker through Intensive Treatment

Batman arrived at the Intensive Treatment Center as Gordon was signing in. Gordon expressed having a tiring night dealing with the police, the media, and Batman after the Joker's kidnapping of the Mayor, yet he was relieved that the Joker was finally back behind bars. Gordon witnessed the Joker's escape and Batman's unsuccessful attempt to capture him. With the Joker in control of security, Gordon was trapped in the Intensive Care Unit along with Frank Boles. Unbeknownst to Gordon, Boles was secretly working with the Joker, knocked Gordon out, and brought him to Harley Quinn in order to keep Batman from following them. Harley took Gordon to the Batmobile in which a struggle took place. Gordon purposely dropped his pipe by the Batmobile, and left a trail of tobacco that lead to his holding place at the Medical Facility.

Batman, followed Gordon's tobacco, then saw Gordon clinging onto a grate, and was pulled by someone. Gordon begged for help, but then lost his grip. He was later found lying against a wall. Batman checked for a pulse: he failed to detect any. After he left Gordon, Batman attempted to contact Oracle, but a ghastly voice said: "I'm sorry, the number you have dialed isn't unavailable. Please leave a message after the tone." Batman entered the Morgue, but was told to exit. Batman then found himself in the same room, "meeting" his deadparents. Then Scarecrow attacked Batman, and hunted him down. Batman defeated Scarecrow, and found a dead Arkham Guard in the place of "Gordon". After he realized that he was madly hallucinating, Batman continued the search for Gordon. Later, Batman found Gordon, but had to defeat some of Joker's Henchmen undetected.

Batman then knocked Quinn unconscious. After being rescued, Gordon said that he had overheard that they were holding someone nearby. When they opened up the room, Bane was revealed to be inside. Batman ordered Gordon to escape as Bane attacked him. Gordon made his way to the surface and regrouped with Batman after the battle. Suddenly, Bane smashed his way to the surface, and attacked Batman once again before he was incapacitated after the Batmobile smashed him into the Gotham River. Batman instructed Gordon to go back to Gotham City via boat, as the people of Gotham would need him and that he'd be much safer. Gordon reluctantly agreed and left Arkham Island along with a security guard.

Somewhere along the journey back to Gotham, Gordon was recaptured by the Joker's Henchmen and taken to the Visitor's Center. There, he was tied up by the Joker and revealed to Batman when he entered the Joker's Throne Room. The Joker planned to turn Gordon into a Titan Henchman, using his dart gun, but Batman jumped in the way of the dart himself, and subjected himself to the Titan Formula. Upon Joker overdosing himself with Titan Formula after Batman had refused to give in to the infection, Gordon was then tied to a sparking chair and was forced to act as the "special guest referee" to Titan-Joker and Batman's fight. After Batman defeated the Joker, Gordon was set free, orchestrated the police attack force, infiltrated Arkham Asylum, and updated Batman with the current status of the island. After he checked in with Barbara, Gordon suddenly received a police radio message that detailed that Two-Face was in the process of robbing the Second National Bank. Batman overheard the message and raced off to the scene in the Batwing.

―James Gordon as Batman carries Joker's dead body out of Arkham City [src]

Commissioner Gordon was very skeptical of the development of Arkham City and the actions of the recently elected Mayor, Quincy Sharp. Gordon attempted to inquire about the project, only to be shot down directly or locked in red tape that allegedly prevented him from learning any answers. Because of that, Gordon decided to send a covert team of operatives into Arkham City to investigate and report back to him. Gordon selected ten officers from the 13th Precinct, his best of the best, and sent them into Arkham City to obtain information. After Bruce Wayne was abducted into Arkham City, he could be heard on the radio mentioning to get Wayne out of there and to stop bringing any new prisoners into Arkham City.

Gordon securing Arkham City

Following the announcement that Protocol 10 was about to be activated, Oracle informed Batman that her father had been called to a meeting of the City Council regarding what was going on. Gordon deployed officers to Arkham City, but they were not able to gain entry due to the security.

While Batman climbed Wonder Tower, Hugo Strange sent TYGER Security to Wayne Manor in order to uncover more of Batman's secrets, only for them to be subdued by Robin and Nightwing. That was the final straw for Gordon, and he went to Arkham City to standby for a order that he knew he would be given: arresting Strange and closing Arkham City. Gordon came to the main entrance, waited for word from Batman, and was intent on leading from the front lines.

As a result, Gordon was present when the Arkham City Gates finally opened and Batman emerged, carrying the lifeless body of the Joker. Confused and suspicious, Gordon asked Batman what happened, but the Dark Knight remained silent. After he knew that his men would tear the Joker's body to shreds, Gordon immediately took the corpse and sent his men into Arkham City to begin evacuating the megaprison, while he also told his wife to leave town for a few weeks and knew that the Joker's thugs would be after her.

For two weeks, Arkham City was being closed down by SWAT, Gordon hid the Joker in any possible hiding place, but eventually returned to Arkham City when four police officers were taken hostage by Quinn. After he summoned Batman to the Industrial District, Gordon kept the area under lockdown for two days while Batman went missing and Robin rescued him. Eventually gaining access to the area, Gordon ran to the Shipyard as the whole place went up in flames due to Quinn's bomb exploding, and transported a knocked-out Harley to the GCPD Holding Cells while Arkham Asylum was reopening.

When Arkham Island was bombed due to the Joker's planning before his death, Batman was thought to have perished. As Gordon found out, he ordered Bullock to make sure that the news did not get leaked to Gotham, even if that meant keeping the news staff locked up for the night. As Gordon lost hope of protecting his city, he received a phone call from none other than Batman, though Batman never revealed how he had survived such a chaotic explosion. Batman and Gordon finally met at the Morgue and cremate Joker's body.

After the Joker's death, the crime rate in Gotham dropped dramatically, but Gordon and Batman would remain vigilant, expecting another one of the various supervillains to make a move. At some point before that Halloween, Gordon was told to visit the disused Panessa Studios by Batman. Arriving by chopper, Gordon entered the building via the roof, eventually making his way into a facility housing four individuals reported missing. Shortly after, Batman arrived and told Gordon that each of the individuals were infected with the Joker's blood, causing them to develop some of his personal traits. Despite there being five people, Gordon noticed that only four were locked up: Albert King, Johnny Charisma, Christina Bell and Henry Adams (the latter of which seemed to be immune).

When Scarecrow attacked Gotham, Gordon and the GCPD helped evacuate civilians from the city and set out to track down the criminal. Whilst waiting for Batman to arrive, Gordon talked with Barbara on the phone, though be believed that she had fled the city. When the Dark Knight arrived, Gordon told him about the information they had been getting and told him about an armored vehicle the GCPD had been chasing. Given a communicator, Gordon received a call about one of his officers being attacked in Chinatown and asked Batman to investigate, only to find the vigilante had disappeared.

Gordon later appeared amongst the officers in the precinct, where he tried to call for reinforcements to help them. When Batman arrived with Poison Ivy, he mused how they now had one less problem to deal with and had officers place her in the containment cell. After another failed attempt to call for the national guard, he and Aaron Cash gave him a series of crime reports they had received before the riots and, having been unable to investigate in time, asked him to do so.

After Batman was able to locate Scarecrow at Ace Chemicals, he informed Gordon and told him to bring as many officers as they could spare. When the vigilante arrived, he ordered the officers to investigate, only for the bridge to be destroyed by one of Scarecrow's allies, theArkham Knight. Forced to retreat by the mercenary's remote controlled tanks, Gordon and his officers stayed behind whilst Batman investigated the plant. After Batman returned two surviving members of a skeleton crew sent in to investigate, Gordon and his officers returned to the headquarters whilst the vigilante pursued after Scarecrow.

When the Arkham Knight's militia overtook the city, Gordon and his officers were able to return to the GCPD Headquarters just before they were able to capture them. When Batman returned, Gordon learnt that Scarecrow had kidnapped Barbara and was being kept somewhere in Gotham. Blinded by anger, Gordon left to go to the Clock Tower, during which he was chased by the Arkham Knight's men. After Batman was able to cripple their vehicles, he accepted a lift from the vigilante and waited in the Batmobile whilst he dealt with men left to guard Barbara's apartment.

After Batman defeated the last of the mercenaries, Gordon entered the Clock Tower and started looking for clues to where they had taken her. However, driven by hallucinations of the Joker, Batman revealed that she had been working with him as the data-broker Oracle. Shocked at the reveal and feeling betrayed, Gordon quickly realized that Scarecrow had kidnapped his daughter for her connection to Batman. He quickly left the Clock Tower and cut his ties to the vigilante, telling him to stay away from his family.

Gordon would not return to the GCPD headquarters whilst he searched for Barbara, though would later be captured by Scarecrow and the militia. Under threat of his daughter's life, he was forced to cooperate with the criminal and, using the GCPD's SWAT channel, contacted Batman to tell him the duo's location: Killinger Department Store. Gordon was kept in the building's main hall under surveillance of the militia, until Batman arrived and defeated them. Gordon also witnessed the battle between Batman and the Arkham Knight, during which the latter revealed both his identity and Batman's. After the Knight's defeat, Gordon was freed and lead Batman to Scarecrow, who was hiding on the building's rooftop. During the journey up, he acknowledged that he was Bruce Wayne and apologized for what his upcoming actions.

Upon arriving, on the rooftops, Gordon initially held Scarecrow at gunpoint, though soon turned it onto Batman. As Scarecrow revealed Barbara, whom Batman had believed to be dead, Gordon tried to negotiate their freedom, only to learn that the criminal had no intention to let them go. With no other choice, Gordon shot Batman's chest and caused the vigilante to fall off the roof, though knew his armor would protect him. As he was held down by the militia, Gordon watched helplessly as Scarecrow threw Barbara off the building and was subsequently saved by Batman. Gordon was later forced to take Scarecrow to Panessa Studios, where they found Robin locked up in one of the cells. Scarecrow would take the Boy Wonder hostage and threatened to kill both of them unless Batman gave himself up.

Taken to the long abandoned Arkham Asylum, Gordon and Robin were held in the Mansion's main hall until Batman finally arrived. Scarecrow, believing that Gotham will panic if Batman was unmasked, forced Gordon to do so on live television. Though the commissioner initially refused, he relented after the criminal shot Robin. With Batman's permission, he unmasked the Dark Knight, revealing his identity of Bruce Wayne to the world. Gordon would only watch as Scarecrow injected Wayne with his fear toxin, though this would only cause the Joker, who's untreated blood was finally taking control, to reemerge and scare the criminal. When Batman finally broke free and injected Scarecrow with his toxin, Gordon knocked him out as he tried to flee and bid his final farewell to the vigilante.

After Batman managed to track down the last of his rogues gallery and left to return home, Gordon ordered his men to retake Gotham and catch the last of the rioters. After Bruce Wayne's supposed death, Gordon retired as Commissioner and began running for the position of Mayor of Gotham, eventually obtaining the position. Some time after the events of that fateful night, he visited the GCPD headquarters, where he looked upon the remains of the destroyed Batsignal. A short time later, he left to attend the wedding of Barbara and Tim Drake.

At the beginning of "Harley Quinn's Revenge", if the player talks to Gordon he mentions that they should discuss "that other problem" at some point. Though he presumably meant Batman's apparent guilt over Joker's death, this same problem is later dealt with in the six comic part Arkham City: End Game, that is set after Harley Quinn's Revenge.

Oddly, it seems that Jim Gordon looks younger in Arkham Knight as opposed to Arkham Asylum or Arkham City.